====== MUMmer ======
MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence.
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This package provides an efficient suffix tree library, seed-and-extend alignment, SNP detection, repeat detection, and visualization tools.
* Install
apt-get install csh
cd /root/
wget http://garr.dl.sourceforge.net/project/mummer/mummer/3.23/MUMmer3.23.tar.gz
tar -xvzf MUMmer3.23.tar.gz
mv MUMmer3.23 /usr/local/
cd /usr/local/MUMmer3.23/
make check
make install
ln -s /usr/local/MUMmer3.23/nucmer /usr/local/bin/
ln -s /usr/local/MUMmer3.23/show-coords /usr/local/bin/
ln -s /usr/local/MUMmer3.23/delta-filter /usr/local/bin/
chown -R root:root /usr/local/MUMmer3.23
* Test
nucmer -h
USAGE: nucmer [options]
DESCRIPTION:
nucmer generates nucleotide alignments between two mutli-FASTA input
files. The out.delta output file lists the distance between insertions
and deletions that produce maximal scoring alignments between each
sequence. The show-* utilities know how to read this format.
MANDATORY:
Reference Set the input reference multi-FASTA filename
Query Set the input query multi-FASTA filename
OPTIONS:
--mum Use anchor matches that are unique in both the reference
and query
--mumcand Same as --mumreference
--mumreference Use anchor matches that are unique in in the reference
but not necessarily unique in the query (default behavior)
--maxmatch Use all anchor matches regardless of their uniqueness
-b|breaklen Set the distance an alignment extension will attempt to
extend poor scoring regions before giving up (default 200)
--[no]banded Enforce absolute banding of dynamic programming matrix
based on diagdiff parameter EXPERIMENTAL (default no)
-c|mincluster Sets the minimum length of a cluster of matches (default 65)
--[no]delta Toggle the creation of the delta file (default --delta)
--depend Print the dependency information and exit
-D|diagdiff Set the maximum diagonal difference between two adjacent
anchors in a cluster (default 5)
-d|diagfactor Set the maximum diagonal difference between two adjacent
anchors in a cluster as a differential fraction of the gap
length (default 0.12)
--[no]extend Toggle the cluster extension step (default --extend)
-f
--forward Use only the forward strand of the Query sequences
-g|maxgap Set the maximum gap between two adjacent matches in a
cluster (default 90)
-h
--help Display help information and exit
-l|minmatch Set the minimum length of a single match (default 20)
-o
--coords Automatically generate the original NUCmer1.1 coords
output file using the 'show-coords' program
--[no]optimize Toggle alignment score optimization, i.e. if an alignment
extension reaches the end of a sequence, it will backtrack
to optimize the alignment score instead of terminating the
alignment at the end of the sequence (default --optimize)
-p|prefix Set the prefix of the output files (default "out")
-r
--reverse Use only the reverse complement of the Query sequences
--[no]simplify Simplify alignments by removing shadowed clusters. Turn
this option off if aligning a sequence to itself to look
for repeats (default --simplify)
-V
--version Display the version information and exit